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* add check of laser antenna position
* implement axel suggestions
* disable laser if antenna is out the box
* fix bug
* Update Source/Particles/LaserParticleContainer.cpp
* implement neil's solution
* remove unnecessary include
* fix initial status of m_enabled
* adding back a check
* add back check
* add back check
* removed unnecessary comment
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
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* Add option to not dump first and last timestep
* Add new function MultiDiagnostics::FilterComputePackFlushLastTimestep
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Update AMReX to https://github.com/AMReX-Codes/amrex/commit/c797f6b6979aea63cc6bda574765c29ba89e7b9c
No changes im PICSAR since last update.
```
./Tools/Release/updatePICSAR.py
./Tools/Release/updateAMReX.py
```
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* Add multi-line example
* Replace newlines and following whitespaces by single whitespaces
* Update Source/Diagnostics/ReducedDiags/FieldReduction.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Update AMReX to https://github.com/AMReX-Codes/amrex/commit/501626901f500b45fce5102c01d15cd8f74c7187
```
./Tools/Release/updateAMReX.py
```
Updated to include https://github.com/AMReX-Codes/amrex/pull/2116
This PR mitigates:
- do no allocated managed memory for received buffers as managed
(with preferred location on-device): they are used only on host
and caused crases with `amrex.the_arena_is_managed=0`
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Avoid relying on managed memory usage in Silver-Mueller boundary
conditions. Previously, we initialized the coefficients on the
host, copied them to device and then accidentially used the
device memory on the host again, as we calculated some constants.
This now keeps the initial host-memory around so we can use it
for host-only operations.
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* Fix Offset: PushPX -> evolve_opt
Comparing to the `doParticlePush()` above, the `ux`/`uy`/`uz` SoA
attributes seem to lack the particle offset in `PushPX`.
Also simplifies the offset calculation to reside off-kernel, which
saves 8 bytes cmem and some index indirection logic for the compiler.
* RigidInjected Particle: Fix Offset
Looks like this is missing here, too?
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This fixes the `ion_map_ids` atom-to-number object:
- declare static, so the file can be included in multiple
translation units
- use `.at()`:
- missing entries do not cause an insertion
- missing entries will throw
- access is `const`, so we can declare the whole object
`static const` as well.
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* Add Field Momentum To Reduced Diagnostics
* Add Particle Momentum To Reduced Diagnostics
* Cover Particle/Field Momentum in CI Test reduced_diags
* Clean Up Implementation of Photons Case
* Fix Bug in Field Momentum and Improve Analysis of CI Test
* Fix 'includes' Following @ax3l's Suggestions
* Interpolate On The Fly, Do Not Allocate Cell-Centered MultiFabs
* Update/Improve Docs
* Fix include, Remove Unused Variable
* Write Total Momentum Divided by Sum of Weights, Test Output
* Write Total Energy Divided by Sum of Weights, Test Output
* Divide by Wtot Only if Not Zero
* Use New Tuple-Level Reductions Available in AMReX
* Use Tuple-level Reduction for Field Momentum
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Fix .rst block highlighting
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* KernelTimer: Fix Cost Use-After-Free
AMReX' ParallelFor is async, the free of the cost function occurs too
early can can lead to use-after-free's from the kernel.
* CMake: WarpX_GPUCLOCK on CUDA/HIP
Make conditional on supported backends.
* Add addition to global cost array
As we abstracted this from the original research prototypes
(https://doi.org/10.5281/zenodo.4708449) to merge this to mainline in
1406, we forgot to add the addition to `*costs` at this point.
Measurements were done with the code linked in the zenodo archive.
* Cleaning: Move m_cost assignment more in
Not too important, but with a default nullptr now possible.
* synchronize -> streamSynchronize
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
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* added ReadBCParams() function call to python execution and added a test of the electrostatic solver executing from python
* added separate specification of particle boundary conditions in picmi setup and adjusted the inputs for existing tests to follow the new practice
* updated input for rz PICMI test and renamed the electrostatic test to follow standard practice
* added arguments for particle boundary conditions to Langmuir RZ test
* added dictionary to picmi.py to map from picmistandard field boundary condition specifications to that of WarpX
* fixes for failing unit tests; added key, pair 'none' to picmi dictionary of field BCs
* also using 'none' for upper boundary condition for RZ test Python_Langmuir_rz_multimode
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* Added injection of a thermal flux from the domain surface
* Major fixes to NFluxPerCell injection
* Small fixes and clean up
* Fixed 'if WARPX_DIMS_RZ' to use ifdef
* Small fix to flux_normal_axis error message
* Fix typo
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Disable Separable Compilation (GPU)
Disable relocatable device code (RDC) aka "separable compilation".
We do not need it unless we use in situ vis.
This addresses issues with CUDA 11.3.0 on Perlmutter, reduces build
complexity and can potentially create more efficient code.
* Update AMReX
Update to eb2fb8eb11d4df88d5b6c04a68f2971a6c3b97f0, so we
include https://github.com/AMReX-Codes/amrex/pull/2083
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Fix a build error with the latest AMReX version due to a missing include.
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* CMake 3.20+ and CUDA: Modernized AMReX
Use modernized AMReX logic for CUDA builds with CMake 3.20+ as
supported by the latest AMReX updates.
* Resampling Trigger: Missing Include
AMReX update triggered missing include:
```
Source/Particles/Resampling/ResamplingTrigger.H(42):
error: namespace "amrex" has no member "Real"
```
* Update AMReX
Update AMReX to f7fd082bc8ab099d42784f69d6fe49dea3d388a7
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* openPMD: Expose ADIOS2 Operators (Compressors)
Expose ADIOS2 Operators (at the moment: one operator max) in WarpX
inputs. This allows the user to select ZFP or Blosc compression
without changing the input file.
We can later on define short-hand notions for this. For now we give
the parameters control out for the expert user and document good
examples.
* Rename: adios2_operator (openPMD)
In that scheme, this only works with ADIOS2 atm.
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* AMReX/PICSAR: 21.06
* WarpX: 21.06
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* Docs: Ookami (Stony Brook)
Add Ookami build instructions.
* Add Suggestions from Luca
Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
* Add 4x12 MPI/OMP
ups, forgot to add
* Ookami: Finalize Batch & Storage
Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
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* improve error msg
* eliminate final dot
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Fix a warning from AMReX by migrating to the newer, recommended
interface.
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* Use Python Indexing in Reduced Diags Headers
* Use Automatic Counter For Column Numbers
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crashes if missing
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Update instructions to fix new errors
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* Added new option <diag>.openpmd_encoding, which can be either file/group/variable
With the encoding being group/variable, there will be one file generated for all
iterations.
* fixed tab
* fixed style
* backward compatibility for openpmd-api versions < 0.14
* eol
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* used inline instead of lamba, encoding decision is moved up at FlushFormatOpenPMD
* making file based the default so scripts can work as is
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Unify defaults of variables
Co-authored-by: Junmin Gu <junmin@login1.summit.olcf.ornl.gov>
Co-authored-by: Junmin Gu <junmin@login3.summit.olcf.ornl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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solve, so that the potential of the previous step is used as a starting guess for the solution of the Poisson equation. (#1968)
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* Follow up on PR #1944
* Fix Bug, Use Better Parser Syntax
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* Docs: Spock (OLCF)
Add an initial instruction on how to build on Spock (OLCF)
for AMD rocm GPUs (HIP).
This works around the missing Cray `PrgEnv-hip` that could be used
with the compiler wrappers.
* Missing -L: Via $CRAYLIBS_X86_64
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
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* Add generic field reduction reduced diag
* Make ComputeFieldReduction public
* Apply suggestions from code review
* Apply suggestions from Luca and Edoardo
* Fix syntax error
* Fix typo in example input file
Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
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* CI: Cancel Prev. Build on Push
Save CI resources by canceling already running or waiting builds if
a PR is updated.
GH Action Ref.:
https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
Azure Pipelines Ref.:
https://docs.microsoft.com/en-us/azure/devops/pipelines/yaml-schema?view=azure-devops&tabs=schema%2Cparameter-schema
(Note: the default seems to be not to be "on" as documented)
* GH Action: Revert Concurrency / Cancel
Somehow stuck in CI, seems to be more to it.
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If `warpx.eb_implicit_function = ...` is present in input parameters, Parser
will be used to initialize EB. For example,
```
warpx.eb_implicit_function = "max(max(max(x-0.5,-0.5-x), max(y-0.5,-0.5-y)), max(z-0.5,-0.5-z))"
```
specifies a box with boundaries at x=+-0.5, y=+-0.5 and z=+-0.5 and regular
domain inside the box.
```
warpx.eb_implicit_function = "-(x**2+y**2+z**2-0.2**2)"
```
specifies a solid sphere at (0,0,0) with a radius of 0.2.
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* Call FillBoundary before momentum half-push at last timestep
* Call FillBoundary before momentum half-push at last timestep
* Update benchmarks
* Update benchmarks again
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* Add ComputeMaxStep() function in WarpXInitData
* Avoid overflow in the static_cast
* Change overflow handling and update stop_time constistently with max_step
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* Read boundary and set periodicity, enumerate BC types, added support for periodic
* separate particle and field boudnary structs
* PEC Etangential Bnormal and setting default pml=0
* eol
* add PEC and FieldBoundary routines
* eol
* remove duplicate struct
* update guard cells for PEC
* host device functions
* remove duplicate function
* fix compilation error by adding ;
* temporary logic to set PEC boundary
* eol
* add documentation for PEC and abort if PEC is used for RZ
* documentation for PEC functions
* remove print statements
* Adding field CI test for PEC for 3D with and without MR
* fix eol
* Apply suggestions from code review
* Update Docs/source/usage/parameters.rst
* Update Source/BoundaryConditions/WarpX_PEC.cpp
* particle PEC CI test
* rename analysis scripts for PEC
* use iside == 0 as condition
* ParallelFor over guard cells. Set field values on boundary and guard in the kernel
* ijk_guard not needed anymore
* remove unnecessary nbody generated by yt
* pi and clight are built-in
* cleanup
* eol
* fix bug in computing ig and ijk_valid
* bug fix in guard-cell update in PEC changes benchmark for particles
* fix bug in the ig compute
* reset particle PEC benchmark
* fix logic to set PEC with current interface
* adding a none type for RZ
* reset benchmarks for 2dLaserInjection, 2dgalilean_hybrid and 2dcomoving CI tests due to differences in PEC reflection
* ensure noz shape factor is used for RZ and k=0 for RZ
* fix XZ/RZ logic for Ey,Etheta,By,Btheta. Add ncomponent for RZ, generically.
* fix the field update for corner cases and mixed boundaries. rename ijk_valid to ijk_mirror since ijk_mirror need not be in valid region
* set GuardCell and Boundary cell flags
* fix compilation bug
* suppress unused variable warning
* eol whitespace
* fix doc
* Apply suggestions from code review
Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov>
* RZ abort message
* reset benchmark after fixing guard-cell updates
* fix typo
* RZ doc
* Update Source/Utils/WarpXUtil.cpp
* Update Examples/Tests/PEC/inputs_particle_PEC_3d
* changes suggested from code-review
* set Enormal and Btangential in guard cell across PEC boundary
* add more info about guard cell update in the docs
* fix typo
* ijk mirror only if ig>0
* update benchmarks
* ignore unused k
* temporarily revert guardcell damping for Cartesian
* fix typo
* dont set Etangential and Bnormal to zero if field is not nodal on boundary
* set bindary int as boolean
* fix high to hi
* set default nox to 1
* particle shape for PEC test
* update benchmarks for 2D comoving and galilean
* reset benchmark for RZ test-cases
* Add in benchmarks generated by @EZoni
* Changing transverse boundaries to periodic for psatd galilean cases
* resetting benchmark for comoving_hybrid_2d and galilean_hybrid_2d
* at-least one guard cell must be filled for PEC
* abort if PEC is used for PSATD
* use new boundary interface to set none for rmin and rmax, since pec does not work for psatd
* Update Source/WarpX.cpp
* add doc mentioning PEC does not work for PSATD
* missing semicolon
* Update Source/BoundaryConditions/WarpX_PEC.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/BoundaryConditions/WarpX_PEC.H
* lengthy comment for normal and tangential components at domain boundaries
* eol fix
* grammar
* field_hi
* reset benchmarks
Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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The weighting attributes of the particle "weighting" record are fixed
by the standard. This fixes their values.
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kzhu-ME
Axel Huebl
Luca Fedeli
Neïl Zaim
David Grote
Andrew Myers
peterscherpelz
Edoardo Zoni
roelof-groenewald
guj
Revathi Jambunathan
Weiqun Zhang
